Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli

Proper phosphate signaling is essential for robust growth of Escherichia coli and many other bacteria. The phosphate signal is mediated by a classic two component signal system composed of PhoR and PhoB.

ibutions SGG planned, performed experiments, prepared, and edited the manuscript JM performed DCA, helped with analysis of data, and aided in preparing the manuscript TD, TR, and ME helped in the scanning mutagenesis PR helped with bioinformatic experimental planning and analysis WRM designed experiments, conducted experiments, aided in data analysis, and aided in preparing and editing the manuscript Acknowledgements We thank Kathryn Hanks, Alex Cummock, Evan Christensen, Bethany Evans, Gregory Bowden, and Michael Barrus for help with sequence collection and mutant characterization This work was supported by Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences Declarations The publication costs for this article were funded by the Department of Microbiology and Molecular Biology at Brigham Young University, the College of Life Sciences at Brigham Young University, and the Public Health Service grant R15GM96222 from the National Institute of General Medical Sciences Gardner et al BMC Genetics 2015, 16(Suppl 2):S2 http://www.biomedcentral.com/1471-2156/16/S2/S2 Page 11 of 11 This article has been published as part of BMC Genetics Volume 16 Supplement 2, 2015: Selected articles from The 11th Annual Biotechnology and Bioinformatics Symposium (BIOT-2014): Genetics The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcgenet/supplements/16/S2 19 Authors’ details Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT, USA 2Department of Biology, Brigham Young University, Provo, UT, USA 20 Published: 23 April 2015 21 References Wanner BL: Phosphorus assimilation and control of the phosphate regulon In Escherichia coli and Salmonella: cellular and molecular biology Washington D C.: American Society for Microbiology;Neidhardt FC, III RC, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE 1996:1357-1381 Chekabab SM, Harel J, Dozois CM: Interplay between genetic regulation of phosphate homeostasis and bacterial virulence Virulence 2014, 5(5) Lamarche MG, Wanner BL, Crepin S, Harel J: The phosphate regulon and bacterial virulence: a regulatory network connecting phosphate homeostasis and pathogenesis FEMS Microbiol Rev 2008, 32(3):461-473 Taylor BL, Zhulin IB: PAS domains: internal sensors of oxygen, redox potential, and light Microbiology and molecular biology reviews : MMBR 1999, 63(2):479-506 Steed PM, Wanner BL: Use of the rep technique for allele replacement to construct mutants with deletions of the pstSCAB-phoU operon: evidence of a new role for the PhoU protein in the phosphate regulon J Bacteriol 1993, 175(21):6797-6809 Haldimann A, Daniels LL, Wanner BL: Use of new methods for construction of tightly regulated arabinose and rhamnose promoter fusions in studies of the Escherichia coli phosphate regulon J Bacteriol 1998, 180(5):1277-1286 Rice CD, Pollard JE, Lewis ZT, McCleary WR: Employment of a promoterswapping technique shows that PhoU modulates the activity of the PstSCAB2 ABC transporter in Escherichia coli Appl Environ Microbiol 2009, 75(3):573-582 Gardner SG, Johns KD, Tanner R, McCleary WR: The PhoU protein from Escherichia coli interacts with PhoR, PstB, and metals to form a phosphate-signaling complex at the membrane J Bacteriol 2014, 196(9):1741-1752 Buron-Barral MC, Gosink KK, Parkinson JS: Loss- and gain-of-function mutations in the F1-HAMP region of the Escherichia coli aerotaxis transducer Aer J Bacteriol 2006, 188(10):3477-3486 10 Studdert CA, Parkinson JS: Insights into the organization and dynamics of bacterial chemoreceptor clusters through in vivo crosslinking studies Proceedings of the National Academy of Sciences of the United States of America 2005, 102(43):15623-15628 11 Datsenko KA, Wanner BL: One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products Proc Natl Acad Sci USA 2000, 97:6640-6645 12 Kozakov D, Brenke R, Comeau SR, Vajda S: PIPER: an FFT-based protein docking program with pairwise potentials Proteins 2006, 65(2):392-406 13 Comeau SR, Gatchell DW, Vajda S, Camacho CJ: ClusPro: an automated docking and discrimination method for the prediction of protein complexes Bioinformatics 2004, 20(1):45-50 14 Comeau SR, Gatchell DW, Vajda S, Camacho CJ: ClusPro: a fully automated algorithm for protein-protein docking Nucleic acids research 2004, 32(Web Server):W96-99 15 Kozakov D, Beglov D, Bohnuud T, Mottarella S, Xia B, Hall DR, Vajda S: How good is automated protein docking? 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Silhavy TJ, Wingreen NS: Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis Genetics 2013, 195(2):443-455 Liu Y, Eyal E, Bahar I: Analysis. .. Bacteriol 2003, 185:1112-1115 doi:10.1186/1471-2156-16-S2-S2 Cite this article as: Gardner et al.: Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate. .. transport mutants of Escherichia coli J Bacteriol 1981, 145(3):1249-1256 Amemura M, Shinagawa H, Makino K, Otsuji N, Nakata A: Cloning of and complementation tests with alkaline phosphatase regulatory